In mid-2000 Masao Inoue left All Japan Pro Wrestling along with all but two All Japan native workers to join Mitsuharu Misawa's newly formed Pro Wrestling Noah. Inoue and Honda were still the All Asia Tag Team champions so the titles were vacated when they left.

Inoue was a founding member of the Dark Agents stable along with Akitoshi Saito and Takashi Sugiura. He would be second-in-command to Saito. Inoue generally spent his time near the bottom card, not receiving very many high profile matches. After several years of struggling to make it up the card, Inoue and seven other NOAH wrestlers were given a huge opportunity to main event a Tokyo Nippon Budokan event. GHC Heavyweight ChampionJun Akiyama proposed a tournament to determine his next challenger. Masao Inoue shocked many wrestling fans by beating rookie Shuhei Taniguchi, Takuma Sano, and finally stablemate Akitoshi Saito to win the tournament. Inoue faced Akiyama in an emotional match and lasted over 23 minutes before falling to the wrist-clutch Exploder. After showing little promise in NOAH's early days, Masao Inoue greatly improved his stock in the company.